The ability to increase the number of analyses being carried out at any given time by a given system has been a key component to increasing the utility and extending the lifespan of analytical systems. In particular, by increasing the multiplex factor of analyses with a given system, one can increase the overall throughput of the system, thereby increasing its usefulness while decreasing the costs associated with that use.
In optical analyses, increasing multiplex often poses increased difficulties, as it may require more complex optical systems, increased illumination or detection capabilities, and new reaction containment strategies. In some cases, systems seek to increase multiplex by many fold, and even orders of magnitude, which further implicate these considerations. Likewise, in certain cases, the analytical environment for which the systems are to be used is so highly sensitive that variations among different analyses in a given system may not be tolerable. These goals are often at odds with a brute force approach of simply making systems bigger and of higher power, as such steps often give rise to even greater consequences, e.g., in inter reaction cross-talk, decreased signal to noise ratios resulting from either or both of lower signal and higher noise, and the like.
For optical systems having arrays of optical confinements, effectively directing excitation light to the optical confinement, and effectively collecting light emitted by the optical confinement can increase efficiency. In some cases, the light can be directed to and from the optical confinements using optical elements such as micromirrors integral to the substrate comprising the optical confinements. For such systems, the alignment of the optical confinement and the optical elements can be important for the quality of the analysis.
It would therefore be desirable to provide analytical systems that have improved alignment between optical confinements and optical elements integral to the substrate on which the optical confinements are disposed. The present invention meets these and a variety of other needs.